Reversible peptide folding in solution by molecular dynamics simulation

Journal of Molecular Biology

Volumn 280, Issue 5, 1998, Pages 925-932

  Daura, Xavier ^a   Jaun, Bernhard ^a   Seebach, Dieter ^a   Van Gunsteren, Wilfred F ^a   Mark, Alan E ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

Free energy; GROMOS; Molecular dynamics; Peptide folding; peptides

Indexed keywords

PEPTIDE;

ARTICLE; COMPUTER SIMULATION; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STABILITY; THERMODYNAMICS;

EID: 0032584783     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1885     Document Type: Article

References (44)

1. Appella, D. H., Christianson, L. A., Karle, I. L., Powell, D. R. & Gellman, S. H. (1996). β-Peptide foldamers: robust helix formation in a new family of β-amino acid oligomers. J. Am. Chem. Soc. 118, 13071-13072.
2. Appella, D. H., Christianson, L. A., Klein, D. A., Powell, D. R., Huang, X., Barchi, J. J., Jr & Gellman, S. H. (1997). Residue-based control of helix shape in β-peptide oligomers. Nature, 387, 381-384.
3. Borman, S. (1997). β-Peptides: nature improved? Chem. Eng. News, 75, 32-35.
4. Constantine, K. L., Friedrichs, M. S. & Stouch, T. R. (1996). Extensive molecular dynamics simulations of a β-hairpin-forming peptide. Biopolymers, 39, 591-614.
5. Daura, X., van Gunsteren, W. F., Rigo, D., Jaun, B. & Seebach, D. (1997). Studying the stability of a helical β-heptapeptide by molecular dynamics simulations. Chem. Eur. J. 3, 1410-1417.
6. Dill, K. A. (1990). Dominant forces in protein folding. Biochemistry, 29, 7133-7155.
7. Dill, K. A. (1997). Additivity principles in biochemistry. J. Biol. Chem. 272, 701-704.
8. Dill, K. A. & Chan, H. S. (1997). From Levinthal to pathways to funnels. Nature Struct. Biol. 4, 10-19.
9. Dobson, C. M. (1992). Unfolded proteins, compact states and molten globules. Curr. Opin. Struct. Biol. 2, 6-12.
10. Dyson, H. J. & Wright, P. E. (1993). Peptide conformation and protein folding. Curr. Opin. Struct. Biol. 3, 60-65.
11. Eaton, W. A., Thompson, P. A., Chan, C.-K., Hagen, S. J. & Hofrichter, J. (1996). Fast events in protein folding. Structure, 4, 1133-1139.
12. Hermans, J. (1993). Molecular dynamics simulations of helix and turn propensities in model peptides. Curr. Opin. Struct. Biol. 3, 270-276.
13. Hinterman, T. & Seebach, D. (1997). The biological stability of β-peptides: no interactions between α- and β-peptidic structures? Chimia, 50, 244-247.
14. Hubbard, S. J. & Thornton, J. M. (1993). NACCESS, computer program. Department of Biochemistry and Molecular Biology, University College London.
15. Iverson, B. L. (1997). Betas are brought into the fold. Nature, 385, 113-115.
16. Karplus, M. & Sali, A. (1995). Theoretical studies of protein folding and unfolding. Curr. Opin. Struct. Biol. 5, 58-73.
17. Karplus, M. & Shakhnovich, E. (1992). Protein folding: theoretical studies of thermodynamics and dynamics. In Protein Folding (Creighton, T. E., ed.), pp. 127-195, W. H. Freeman & Co., New York.
18. Koert, U. (1997). β-Peptides: novel secondary structures take shape. Agnew. Chem. Int. Ed. Engl. 36, 1836-1837.
19. Kolinski, A. & Skolnick, J. (1994). Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins: Struct. Funct. Genet. 18, 338-352.
20. Kovacs, H., Mark, A. E., Johansson, J. & van Gunsteren, W. F. (1995). The effect of environment on the stability of an integral membrane helix: molecular dynamics simulations of surfractant protein C in chloroform, methanol and water. J. Mol. Biol. 247, 808-822.
21. Krüger, P., Lüke, M. & Szameit, A. (1991). SIMLYS - a software package for trajectory analysis of molecular dynamics simulations. Comput. Phys. Commun. 62, 371-380.
22. Leach, A. R. (1991). A survey of methods for searching the conformational space of small and medium-sized molecules. In Reviews in Computational Chemistry (Lipkowitz, K. B. & Boyd, D. B., eds), vol. 2, pp. 1-55, VCH Publishers, Inc., New York.
23. Mark, A. E. & van Gunsteren, W. F. (1994). Decomposition of the free energy of a system in terms of specific interactions: implication for theoretical and experimental studies. J. Mol. Biol. 240, 167-176.
24. Marshall, G. R., Beusen, D. D. & Nikiforovich, G. V. (1995). Peptide conformation: stability and dynamics. In Peptides: Synthesis, Structures and Applications (Gutte, B., ed.), pp. 193-245, Academic Press, San Diego.
25. Mohanty, D., Elber, R., Thirumalai, D., Beglov, D. & Roux, B. (1997). Kinetics of peptide folding: computer simulations of SYPFDV and peptide variants in water. J. Mol. Biol. 272, 423-442.
26. Neri, D., Billeter, M., Wider, G. & Wüthrich, K. (1992). NMR determination of residual structure in a urea-denatured protein, the 434-repressor. Science, 257, 1559-1563.
27. Pedersen, J. T. & Moult, J. (1997). Protein folding simulations with genetic algorithms and a detailed molecular description. J. Mol. Biol. 269, 240-259.
28. Ripoll, D. R. & Scheraga, H. A. (1988). On the multiple-minima problem in the conformational analysis of polypeptides. II. An electrostatically driven Monte Carlo method-tests on poly(L-alanine). Biopolymers, 27, 1283-1303.
29. Schulz, G. E. (1988). A critical evaluation of methods for prediction of protein secondary structures. Annu. Rev. Biophys. Biophys. Chem. 17, 1-21.
30. Seebach, D., Overhand, M., Kühnle, F. N. M., Martinoni, B., Oberer, L., Hommel, U. & Widmer, H. (1996a). β-Peptides: synthesis by Arndt-Eistert homologation with concomitant peptide coupling. Structure determination by NMR and CD spectroscopy and by X-ray crystallography. Helical secondary structure of a β-hexapeptide in solution and its stability towards pepsin. Helv. Chem. Acta, 79, 913-941.
31. Seebach, D., Ciceri, P. E., Overhand, M., Jaun, B., Rigo, D., Oberer, L., Hommel, U., Amstutz, R. & Widmer, H. (1996b). Probing the helical secondary structure of short-chain β-peptides. Helv. Chim. Acta, 79, 2043-2066.
32. Shortle, D. R. (1996). Structural analysis of non-native states of proteins by NMR methods. Curr. Opin. Struct. Biol. 6, 24-30.
33. Shortle, D., Wang, Y., Gillespie, J. R. & Wrabl, J. O. (1996). Protein folding for realists: a timeless phenomenon. Protein Sci. 5, 991-1000.
34. Smith, L. J., Fiebig, K. M., Schwalbe, H. & Dobson, C. M. (1996). The concept of a random coil. Residual structure in peptides and denatured proteins. Folding Des. 1, R95-R106.
35. Sung, S.-S. (1994). Helix folding simulations with various initial conformations. Biophys. J. 66, 1796-1803.
36. Sung, S.-S. & Wu, X.-W. (1996). Molecular dynamics simulations of synthetic peptide folding. Proteins: Struct. Funct. Genet. 25, 202-214.
37. Thomas, P. D. & Dill, K. A. (1996). Statistical potentials extracted from protein structures: how accurate are they? J. Mol. Biol. 257, 457-469.
38. Thompson, P. A., Eaton, W. A. & Hofrichter, J. (1997). Laser temperature jump study of the helix-coil kinetics of an alanine peptide interpreted with a 'Kinetic Zipper' model. Biochemistry, 36, 9200-9210.
39. Tobias, D. J., Mertz, J. E. & Brooks, C. L., III (1991). Nanosecond time scale folding dynamics of a pentapeptide in water. Biochemistry, 30, 6054-6058.
40. Troyer, J. M. & Cohen, F. E. (1991). Simplified models for understanding and predicting protein structure. In Reviews in Computational Chemistry (Lipkowitz, K. B. & Boyd, D. B., eds), vol. 2, pp. 57-80, VCH Publishers, Inc., New York.
41. van Gunsteren, W. F., Billeter, S. R., Eising, A. A., Hünenberger, P. H., Krüger, P., Mark, A. E., Scott, W. R. P. & Tironi, I. G. (1996). Biomolecular Simulation: The GROMOS96 Manual and User Guide, pp. 1-1024, Vdf Hochschulverlag AG an der ETH Zürich, Zürich.
42. Vieth, M., Kolinski, A., Brooks, C. L., III & Skolnick, J. (1994). Prediction of the folding pathways and structure of the GCN4 leucine zipper. J. Mol. Biol. 237, 361-367.
43. Williams, S., Causgrove, T. P., Gilmanshin, R., Fang, K. S., Callender, R. H., Woodruff, W. H. & Dyer, R. B. (1996). Fast events in protein folding: helix melting and formation in a small peptide. Biochemistry, 35, 691-697.
44. Yue, K. & Dill, K. A. (1996). Folding proteins with a simple energy function and extensive conformational searching. Protein Sci. 5, 254-261.